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Add R script to process data #6

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7cb68cd
Add R script to process data
oliverfanderson Oct 31, 2024
7165629
Update R script
oliverfanderson Nov 8, 2024
c417102
Preprocessed 14 pathways into S/T sets
oliverfanderson Nov 15, 2024
d512be8
Create node-prizes file from sources/targets
oliverfanderson Nov 20, 2024
0293ae4
Process datasets into Prizes with 100 as score
oliverfanderson Dec 4, 2024
cc34678
Processed two new pathways
oliverfanderson Mar 10, 2025
6973c72
Added new improved processing script
oliverfanderson Mar 19, 2025
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4 changes: 4 additions & 0 deletions .gitignore
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Expand Up @@ -160,3 +160,7 @@ cython_debug/
# and can be added to the global gitignore or merged into this file. For a more nuclear
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/
preprocessing/human-interactome/9606.protein.links.full.v12.0.txt
preprocessing/B_cell_activation/.Rhistory
preprocessing/.DS_Store
.DS_Store
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457 changes: 457 additions & 0 deletions preprocessing/Apoptosis_signaling/Apoptosis_signaling_.txt
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1 change: 1 addition & 0 deletions preprocessing/Apoptosis_signaling/DEL-EDGES-Apoptosis_signaling_.txt
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id1 id2
1 change: 1 addition & 0 deletions preprocessing/Apoptosis_signaling/DEL-NODES-Apoptosis_signaling_.txt
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id uniprot
145 changes: 145 additions & 0 deletions preprocessing/Apoptosis_signaling/NODES-Apoptosis_signaling_.txt
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id uniprot string ensembl
ATF1 P18846 9606.ENSP00000262053 ENSG00000123268
ATF2 P15336 9606.ENSP00000264110 ENSG00000115966
TNF P01375 9606.ENSP00000398698 ENSG00000204490
TNF P01375 9606.ENSP00000398698 ENSG00000206439
TNF P01375 9606.ENSP00000398698 ENSG00000228321
TNF P01375 9606.ENSP00000398698 ENSG00000228849
TNF P01375 9606.ENSP00000398698 ENSG00000230108
TNF P01375 9606.ENSP00000398698 ENSG00000223952
TNF P01375 9606.ENSP00000398698 ENSG00000232810
AKT2 P31751 9606.ENSP00000375892 ENSG00000105221
AKT3 Q9Y243 9606.ENSP00000500582 ENSG00000117020
AKT3 Q9Y243 9606.ENSP00000500582 ENSG00000275199
TNFSF10 P50591 9606.ENSP00000241261 ENSG00000121858
AKT1 P31749 9606.ENSP00000451828 ENSG00000142208
MAP3K5 Q99683 9606.ENSP00000351908 ENSG00000197442
MAP2K3 P46734 9606.ENSP00000345083 ENSG00000034152
PRKCG P05129 9606.ENSP00000263431 ENSG00000126583
MAP2K4 P45985 9606.ENSP00000410402 ENSG00000065559
DAXX Q9UER7 9606.ENSP00000266000 ENSG00000204209
DAXX Q9UER7 9606.ENSP00000266000 ENSG00000206206
DAXX Q9UER7 9606.ENSP00000266000 ENSG00000206279
DAXX Q9UER7 9606.ENSP00000266000 ENSG00000231617
DAXX Q9UER7 9606.ENSP00000266000 ENSG00000227046
PRKCH P24723 9606.ENSP00000329127 ENSG00000027075
ENDOG Q14249 9606.ENSP00000361725 ENSG00000167136
PRKCB P05771 9606.ENSP00000496129 ENSG00000166501
PRKCE Q02156 9606.ENSP00000306124 ENSG00000171132
PRKCD Q05655 9606.ENSP00000331602 ENSG00000163932
PRKCA P17252 9606.ENSP00000408695 ENSG00000154229
MADD Q8WXG6 9606.ENSP00000310933 ENSG00000110514
PRKCQ Q04759 9606.ENSP00000263125 ENSG00000065675
ATF7 P17544 9606.ENSP00000399465 ENSG00000170653
TP53 P04637 9606.ENSP00000269305 ENSG00000141510
ATF6 P18850 9606.ENSP00000356919 ENSG00000118217
ATF3 P18847 9606.ENSP00000344352 ENSG00000162772
ATF4 P18848 9606.ENSP00000336790 ENSG00000128272
DIABLO Q9NR28 9606.ENSP00000398495 ENSG00000184047
CREM Q03060 9606.ENSP00000265372 ENSG00000095794
BCL2L10 Q9HD36 9606.ENSP00000453562 ENSG00000137875
BAG4 O95429 9606.ENSP00000287322 ENSG00000156735
BCL2L11 O43521 9606.ENSP00000376943 ENSG00000153094
BAG3 O95817 9606.ENSP00000358081 ENSG00000151929
RIPK1 Q13546 9606.ENSP00000259808 ENSG00000137275
FADD Q13158 9606.ENSP00000301838 ENSG00000168040
MAP2K7 O14733 9606.ENSP00000381070 ENSG00000076984
MCL1 Q07820 9606.ENSP00000358022 ENSG00000143384
HSPA8 P11142 9606.ENSP00000437125 ENSG00000109971
JUN P05412 9606.ENSP00000360266 ENSG00000177606
CRADD P78560 9606.ENSP00000439068 ENSG00000169372
HSPA5 P11021 9606.ENSP00000324173 ENSG00000044574
HSPA6 P17066 9606.ENSP00000310219 ENSG00000173110
TNFRSF10C O14798 9606.ENSP00000349324 ENSG00000173535
EIF2AK2 P19525 9606.ENSP00000233057 ENSG00000055332
TNFRSF10B O14763 9606.ENSP00000276431 ENSG00000120889
TNFRSF10A O00220 9606.ENSP00000221132 ENSG00000104689
HSPA2 P54652 9606.ENSP00000378199 ENSG00000126803
EIF2S1 P05198 9606.ENSP00000256383 ENSG00000134001
IGF2R P11717 9606.ENSP00000349437 ENSG00000197081
NFKB1 P19838 9606.ENSP00000226574 ENSG00000109320
TNFRSF10D Q9UBN6 9606.ENSP00000310263 ENSG00000173530
NFKB2 Q00653 9606.ENSP00000358983 ENSG00000077150
NFKBIA P25963 9606.ENSP00000216797 ENSG00000100906
BCL2 P10415 9606.ENSP00000381185 ENSG00000171791
REL Q04864 9606.ENSP00000295025 ENSG00000162924
CYCS P99999 9606.ENSP00000307786 ENSG00000172115
MAP3K14 Q99558 9606.ENSP00000482657 ENSG00000006062
BCL2L2 Q92843 9606.ENSP00000250405 ENSG00000129473
BCL2L2 Q92843 9606.ENSP00000250405 ENSG00000258643
BCL2L1 Q07817 9606.ENSP00000365230 ENSG00000171552
TRADD Q15628 9606.ENSP00000341268 ENSG00000102871
PIK3CD O00329 9606.ENSP00000366563 ENSG00000171608
FASLG P48023 9606.ENSP00000356694 ENSG00000117560
PIK3CB P42338 9606.ENSP00000501150 ENSG00000051382
PIK3CG P48736 9606.ENSP00000419260 ENSG00000105851
CASP9 P55211 9606.ENSP00000330237 ENSG00000132906
IKBKB O14920 9606.ENSP00000430684 ENSG00000104365
CASP7 P55210 9606.ENSP00000358327 ENSG00000165806
CASP8 Q14790 9606.ENSP00000351273 ENSG00000064012
AIFM1 O95831 9606.ENSP00000287295 ENSG00000156709
CASP10 Q92851 9606.ENSP00000286186 ENSG00000003400
CASP3 P42574 9606.ENSP00000311032 ENSG00000164305
BOK Q9UMX3 9606.ENSP00000314132 ENSG00000176720
MAP4K2 Q12851 9606.ENSP00000294066 ENSG00000168067
CHUK O15111 9606.ENSP00000359424 ENSG00000213341
APAF1 O14727 9606.ENSP00000448165 ENSG00000120868
TRAF2 Q12933 9606.ENSP00000247668 ENSG00000127191
FOS P01100 9606.ENSP00000306245 ENSG00000170345
TNFRSF1B P20333 9606.ENSP00000365435 ENSG00000028137
TNFRSF1A P19438 9606.ENSP00000162749 ENSG00000067182
PIK3CA P42336 9606.ENSP00000263967 ENSG00000121879
LTA P01374 9606.ENSP00000403495 ENSG00000230279
LTA P01374 9606.ENSP00000403495 ENSG00000226979
LTA P01374 9606.ENSP00000403495 ENSG00000231408
TMBIM6 P55061 9606.ENSP00000389277 ENSG00000139644
LTB Q06643 9606.ENSP00000410481 ENSG00000204487
LTB Q06643 9606.ENSP00000410481 ENSG00000206437
LTB Q06643 9606.ENSP00000410481 ENSG00000223448
LTB Q06643 9606.ENSP00000410481 ENSG00000238114
LTB Q06643 9606.ENSP00000410481 ENSG00000227507
LTB Q06643 9606.ENSP00000410481 ENSG00000236925
LTB Q06643 9606.ENSP00000410481 ENSG00000236237
LTB Q06643 9606.ENSP00000410481 ENSG00000231314
BIRC2 Q13490 9606.ENSP00000477613 ENSG00000110330
JDP2 Q8WYK2 9606.ENSP00000267569 ENSG00000140044
BIRC3 Q13489 9606.ENSP00000263464 ENSG00000023445
ATF6B Q99941 9606.ENSP00000364349 ENSG00000168468
ATF6B Q99941 9606.ENSP00000364349 ENSG00000213676
ATF6B Q99941 9606.ENSP00000364349 ENSG00000228628
ATF6B Q99941 9606.ENSP00000364349 ENSG00000234539
XIAP P98170 9606.ENSP00000360242 ENSG00000101966
RELA Q04206 9606.ENSP00000384273 ENSG00000173039
RELB Q01201 9606.ENSP00000221452 ENSG00000104856
MAPK9 P45984 9606.ENSP00000394560 ENSG00000050748
MAPK8 P45983 9606.ENSP00000378974 ENSG00000107643
MAPK1 P28482 9606.ENSP00000215832 ENSG00000100030
BAK1 Q16611 9606.ENSP00000363591 ENSG00000030110
BCL2L2-PABPN1 Q92843 9606.ENSP00000250405 ENSG00000129473
BCL2L2-PABPN1 Q92843 9606.ENSP00000250405 ENSG00000258643
MAP4K3 Q8IVH8 9606.ENSP00000263881 ENSG00000011566
MAPK3 P27361 9606.ENSP00000263025 ENSG00000102882
MAP4K4 O95819 9606.ENSP00000343658 ENSG00000071054
MAP3K1 Q13233 9606.ENSP00000382423 ENSG00000095015
HSPA1L P34931 9606.ENSP00000364805 ENSG00000204390
HSPA1L P34931 9606.ENSP00000364805 ENSG00000206383
HSPA1L P34931 9606.ENSP00000364805 ENSG00000234258
HSPA1L P34931 9606.ENSP00000364805 ENSG00000236251
BIK Q13323 9606.ENSP00000216115 ENSG00000100290
GZMB P10144 9606.ENSP00000216341 ENSG00000100453
CFLAR O15519 9606.ENSP00000312455 ENSG00000003402
GZMH P20718 9606.ENSP00000216338 ENSG00000100450
MAPK10 P53779 NA ENSG00000109339
PRKRA O75569 9606.ENSP00000318176 ENSG00000180228
BAX Q07812 9606.ENSP00000293288 ENSG00000087088
FAS P25445 9606.ENSP00000498466 ENSG00000026103
HSPA1B P0DMV9 NA ENSG00000204388
HSPA1B P0DMV9 NA ENSG00000224501
HSPA1B P0DMV9 NA ENSG00000212866
HSPA1B P0DMV9 NA ENSG00000231555
HSPA1B P0DMV9 NA ENSG00000232804
HSPA1A P0DMV8 9606.ENSP00000364801 ENSG00000204389
HSPA1A P0DMV8 9606.ENSP00000364801 ENSG00000215328
HSPA1A P0DMV8 9606.ENSP00000364801 ENSG00000235941
HSPA1A P0DMV8 9606.ENSP00000364801 ENSG00000234475
HSPA1A P0DMV8 9606.ENSP00000364801 ENSG00000237724
24 changes: 24 additions & 0 deletions preprocessing/Apoptosis_signaling/PRIZES-100-Apoptosis_signaling_.txt
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id prizes active
ATF1 100 true
ATF2 100 true
ATF7 100 true
TP53 100 true
ATF6 100 true
ATF3 100 true
ATF4 100 true
CREM 100 true
JUN 100 true
NFKB1 100 true
NFKB2 100 true
REL 100 true
FOS 100 true
JDP2 100 true
ATF6B 100 true
RELA 100 true
RELB 100 true
TNFRSF10C 100 true
TNFRSF10A 100 true
TNFRSF10D 100 true
TNFRSF1B 100 true
TNFRSF1A 100 true
FAS 100 true
18 changes: 18 additions & 0 deletions preprocessing/Apoptosis_signaling/SOURCES-Apoptosis_signaling_.txt
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id uniprot string ensembl
ATF1 P18846 9606.ENSP00000262053 ENSG00000123268
ATF2 P15336 9606.ENSP00000264110 ENSG00000115966
ATF7 P17544 9606.ENSP00000399465 ENSG00000170653
TP53 P04637 9606.ENSP00000269305 ENSG00000141510
ATF6 P18850 9606.ENSP00000356919 ENSG00000118217
ATF3 P18847 9606.ENSP00000344352 ENSG00000162772
ATF4 P18848 9606.ENSP00000336790 ENSG00000128272
CREM Q03060 9606.ENSP00000265372 ENSG00000095794
JUN P05412 9606.ENSP00000360266 ENSG00000177606
NFKB1 P19838 9606.ENSP00000226574 ENSG00000109320
NFKB2 Q00653 9606.ENSP00000358983 ENSG00000077150
REL Q04864 9606.ENSP00000295025 ENSG00000162924
FOS P01100 9606.ENSP00000306245 ENSG00000170345
JDP2 Q8WYK2 9606.ENSP00000267569 ENSG00000140044
ATF6B Q99941 9606.ENSP00000364349 ENSG00000213676
RELA Q04206 9606.ENSP00000384273 ENSG00000173039
RELB Q01201 9606.ENSP00000221452 ENSG00000104856
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